BMGF - OpenMalaria Workflow and OpenMalariaUtilities R Packages
Project Abstract
OpenMalaria Workflow R Package
The work of the Analytics and Intervention Modelling Group is based on OpenMalaria: an open-source C++ program for simulating malaria epidemiology and the impacts on that epidemiology of interventions against malaria.
OpenMalaria has a very broad range of potential applications, therefore, in order to use it for the simulation of country-specific analyses, such as the simulation of a national strategic plan, the prioritisation of interventions or cost-effectiveness studies, additional tools are required (Runge et al. 2020). Hence, the Swiss TPH team has developed a workflow tool that enables to use OpenMalaria for applied country-specific scenario simulations.
The tool relies on the R programming language, which is widely known among disease modellers and epidemiologists.
The tool is a collection of R functions that enables a user to create a country-specific simulation experiment, run it with OpenMalaria using high performance computing infrastructure, create datasets of the simulation results and calibrate the simulations to setting-specific malaria trends. It also includes a set of functions required to perform cost-effectiveness analyses, such attachment of costing data and optimisation routines.
A public version is currently under development and it will soon be available on the Swiss TPH GitHub.
OpenMalariaUtilities R Package
At the core of our OpenMalaria Workflow is the OpenMalariaUtilities R package which is developed to allow the use of OpenMalaria directly from R. The package has been the main tool used by the Analytics and Intervention Modelling Group since November 2021 and it is now publicly available.
This interactive workflow allows the user to utilize the OpenMalaria modelling suite for specific geographies in an easy-to-use manner. R is used as the primary programming language and the code has been licensed under the GNU General Public License v3.0 (GPL 3). Standardization and modularity are among the main development goals in order to ensure robustness and reproducibility as well as flexibility and versatility.
The OpenMalariaUtilities consists of three modules: i) generating the input for OpenMalaria, ii) running one or more simulations and iii) collecting and aggregating the results.
We believe that the OpenMalariaUtilities R Package greatly lowers the barriers for new modelers to use the powerful OpenMalaria simulation platform which will also foster new input and more engagement in the community.
We are continuing the development and improvement of both R packages as well as their documentation. Releases are publicly available on the Swiss TPH GitHub.
The OpenMalaria Workflow R Package together with the OpenMalariaUtilities R Package are used for the sub-national tailoring of interventions stratification for malaria in support to countries such as Benin, Mozambique, as well as for others.
